PubChem 2019 update: improved access to chemical data
Open accessAbstract
PubChem (https://pubchem.ncbi.nlm.nih.gov) is a key chemical information resource for the biomedical research community. Substantial improvements were made in the past few years. New data content was added, including spectral information, scientific articles mentioning chemicals, and information for food and agricultural chemicals. PubChem released new web interfaces, such as PubChem Target View page, Sources page, Bioactivity dyad pages and Patent View page. PubChem also released a major update to PubChem Widgets and introduced a new programmatic access interface, called PUG-View. This paper describes these new developments in PubChem.
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The use of SMILES avoids the issues of ununified substrate naming between the GEM and BRENDA that original-ecGEM reconstruction pipelines can experience.
“the use of SMILES (matching via the PubChem 48 or MetaNetX 49 databases) avoids the issues of ununified substrate naming between the GEM and BRENDA that original-ecGEM reconstruction pipelines can experience.”
From Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction (2022) · cites this paper as [48]
The ligand details page shows a 2D depiction of the ligand chemical structure, together with synonyms and identifiers from PubChem, Guide to Pharmacology, ChEMBL and DrugCentral.
“A 2D depiction of the ligand chemical structure is shown, together with synonyms and identifiers from PubChem (43), Guide to Pharmacology (44), ChEMBL and DrugCentral.”
From TCRD and pharos 2021: mining the human proteome for disease biology (2021) · cites this paper as [43]
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Cites
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- Authors
- Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky, L., Zhang, J., & Bolton, E. E.
- Affiliations
- National Institutes of Health (US)
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20894, USA
- Corresponding author
- Bolton, Evan E
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2018-10-29
- Volume
- 47
- Issue
- D1
- Pages
- D1102-D1109
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC6324075
- OpenAlex
- W2899070097
- Cited by
- 3,249
- References
- 23
- Citations by year
- 2026: 167 · 2025: 320 · 2024: 354 · 2023: 401 · 2022: 476 · 2021: 704 · 2020: 619 · 2019: 198 · 2018: 1 · 2017: 1
- FWCI
- 285.53
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- public-domain
- Locations
- Nucleic Acids Research (publishedVersion, public-domain)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- Topics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Keywords
- PubChem, chemical information resources, spectral data, bioactivity data, programmatic access, web interface
- MeSH terms
- Animals, Biological Assay, Pharmaceutical Preparations, Humans, Patents as Topic, Structure-Activity Relationship, Molecular Structure, Information Storage and Retrieval, Computational Biology, Internet, Small Molecule Libraries, Drug Discovery, High-Throughput Screening Assays, Databases, Chemical
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